chr6-31253891-C-G

Variant names:

• chr6-31253891-C-G
• rs3095254

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.555 in 151,334 control chromosomes in the GnomAD database, including 24,279 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24279 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.555 AC: 83997 AN: 151216 Hom.: 24282 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.536

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.555 AC: 84010 AN: 151334 Hom.: 24279 Cov.: 31 AF XY: 0.550 AC XY: 40637 AN XY: 73862

African (AFR) AF: 0.437 AC: 18051 AN: 41338

American (AMR) AF: 0.550 AC: 8367 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2095 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2924 AN: 5046

South Asian (SAS) AF: 0.476 AC: 2235 AN: 4694

European-Finnish (FIN) AF: 0.561 AC: 5869 AN: 10464

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42630 AN: 67808

Other (OTH) AF: 0.535 AC: 1121 AN: 2094

Alfa AF: 0.474 Hom.: 1482

Bravo AF: 0.550

Asia WGS AF: 0.517 AC: 1789 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3095254; hg19: chr6-31221668;